Package: pathwayPCA

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathwayPCA_1.3.0.tar.gz

StartedAt: 2020-01-16 07:17:22 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:21:53 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 271.0 seconds

RetCode: 0

Status:  OK

CheckDir: pathwayPCA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathwayPCA_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/pathwayPCA.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathwayPCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathwayPCA’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pathwayPCA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
SE2Tidy        16.520  1.239  17.839
LoadOntoPCs     0.580  0.629  13.672
AESPCA_pVals    0.529  0.597  13.233
SuperPCA_pVals  0.800  0.047  12.552
ExtractAESPCs   0.425  0.396   9.294
getPathPCLs     0.209  0.068  15.042
getPathpVals    0.199  0.063  14.172
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pathwayPCA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘pathwayPCA’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pathwayPCA)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(pathwayPCA)
> 
> test_check("pathwayPCA")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 47 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 23.590   2.639  77.847 

name	user	system	elapsed
AESPCA_pVals	0.529	0.597	13.233
CheckAssay	0	0	0
CheckPwyColl	0.000	0.001	0.001
CheckSampleIDs	0.000	0.001	0.001
Contains	0.002	0.001	0.003
ControlFDR	0.001	0.001	0.001
CreateOmics	0.429	0.103	0.534
CreateOmicsPathway	0.004	0.004	0.009
CreatePathwayCollection	0.010	0.003	0.013
ExtractAESPCs	0.425	0.396	9.294
GumbelMixpValues	0.000	0.001	0.002
IntersectOmicsPwyCollct	0.000	0.001	0.002
JoinPhenoAssay	0.000	0.001	0.000
LoadOntoPCs	0.580	0.629	13.672
OptimGumbelMixParams	0.001	0.001	0.001
PathwaytValues	0.001	0.001	0.002
PermTestCateg	0.000	0.001	0.001
PermTestReg	0.001	0.001	0.002
PermTestSurv	0.001	0.001	0.001
SE2Tidy	16.520	1.239	17.839
SubsetPathwayCollection	0.005	0.003	0.007
SubsetPathwayData	0.251	0.094	0.346
SuperPCA_pVals	0.800	0.047	12.552
TabulatepValues	0.000	0.001	0.002
TransposeAssay	0.161	0.054	0.224
WhichPathways	0.010	0.002	0.012
aespca	0.000	0.000	0.001
coxTrain_fun	0.000	0.001	0.001
getPathPCLs	0.209	0.068	15.042
getPathpVals	0.199	0.063	14.172
get_set_OmicsPathway	1.895	0.917	2.817
get_set_OmicsRegCateg	0.096	0.018	0.113
get_set_OmicsSurv	0.120	0.019	0.139
glmTrain_fun	0.001	0.000	0.001
lars.lsa	0.001	0.000	0.001
mysvd	0.001	0.000	0.001
normalize	0.000	0.000	0.001
olsTrain_fun	0.001	0.001	0.001
pathway_tControl	0.001	0.001	0.002
pathway_tScores	0.001	0.000	0.002
permuteSamps	0.000	0.000	0.001
print.pathwayCollection	0.007	0.002	0.009
read_gmt	0.217	0.005	0.224
show-OmicsPathway-method	0.102	0.007	0.109
superpc.st	0.001	0.001	0.002
superpc.train	0.000	0.001	0.001
write_gmt	0.006	0.001	0.006